[med-svn] [pbdagcon] branch upstream updated (7b1ae4f -> b247711)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch upstream
in repository pbdagcon.

      from  7b1ae4f   Imported Upstream version 0~20160325+ds
       new  b247711   Imported Upstream version 0.3+20161121+ds

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitignore                          |   11 -
 .gitmodules                         |    9 -
 DALIGNER/DB2Falcon.c                |  133 +
 DALIGNER/GNUmakefile                |   30 +
 DALIGNER/HPCdaligner.c              |  543 ++++
 DALIGNER/HPCmapper.c                |  591 ++++
 DALIGNER/LA4Falcon.c                |  802 ++++++
 DALIGNER/LA4Ice.c                   |  568 ++++
 DALIGNER/LAcat.c                    |  157 ++
 DALIGNER/LAcheck.c                  |  310 +++
 DALIGNER/LAdump.c                   |  478 ++++
 DALIGNER/LAindex.c                  |  201 ++
 DALIGNER/LAmerge.c                  |  387 +++
 DALIGNER/LAshow.c                   |  594 ++++
 DALIGNER/LAsort.c                   |  252 ++
 DALIGNER/LAsplit.c                  |  207 ++
 DALIGNER/LICENSE                    |   34 +
 DALIGNER/Makefile                   |   69 +
 DALIGNER/README                     |  395 +++
 DALIGNER/README_PB.md               |    8 +
 DALIGNER/align.c                    | 5112 +++++++++++++++++++++++++++++++++++
 DALIGNER/align.h                    |  335 +++
 DALIGNER/daligner.c                 |  726 +++++
 DALIGNER/daligner_p.c               |    1 +
 DALIGNER/filter.c                   | 2266 ++++++++++++++++
 DALIGNER/filter.h                   |   38 +
 DALIGNER/filter_p.c                 |    2 +
 DALIGNER/py_utils/DAPI.py           |   72 +
 DALIGNER/py_utils/DAPipe.py         |   93 +
 DALIGNER/py_utils/DBLA_to_falcon.py |   42 +
 DALIGNER/py_utils/FALCON_ASM_NOTE   |   27 +
 DALIGNER/py_utils/LAPI.py           |  110 +
 DALIGNER/py_utils/LAPipe.py         |  177 ++
 DAZZ_DB/Catrack.c                   |  259 ++
 DAZZ_DB/DAM2fasta.c                 |  200 ++
 DAZZ_DB/DB.c                        | 1690 ++++++++++++
 DAZZ_DB/DB.h                        |  415 +++
 DAZZ_DB/DB2fasta.c                  |  151 ++
 DAZZ_DB/DB2quiva.c                  |  155 ++
 DAZZ_DB/DBdump.c                    |  720 +++++
 DAZZ_DB/DBdust.c                    |  471 ++++
 DAZZ_DB/DBrm.c                      |   40 +
 DAZZ_DB/DBshow.c                    |  577 ++++
 DAZZ_DB/DBsplit.c                   |  214 ++
 DAZZ_DB/DBstats.c                   |  346 +++
 DAZZ_DB/DBupgrade.Dec.31.2014.c     |   86 +
 DAZZ_DB/DBupgrade.Sep.25.2014.c     |   96 +
 DAZZ_DB/DUSTupgrade.Jan.1.2015.c    |   80 +
 DAZZ_DB/GNUmakefile                 |   33 +
 DAZZ_DB/LICENSE                     |   34 +
 DAZZ_DB/Makefile                    |   70 +
 DAZZ_DB/QV.c                        | 1369 ++++++++++
 DAZZ_DB/QV.h                        |   90 +
 DAZZ_DB/README                      |  459 ++++
 DAZZ_DB/fasta2DAM.c                 |  412 +++
 DAZZ_DB/fasta2DB.c                  |  645 +++++
 DAZZ_DB/quiva2DB.c                  |  347 +++
 DAZZ_DB/simulator.c                 |  421 +++
 configure.py                        |    6 +-
 makefile                            |    2 +-
 test/cpp/.gitignore                 |    2 -
 61 files changed, 24144 insertions(+), 26 deletions(-)
 delete mode 100644 .gitignore
 delete mode 100644 .gitmodules
 create mode 100644 DALIGNER/DB2Falcon.c
 create mode 100644 DALIGNER/GNUmakefile
 create mode 100644 DALIGNER/HPCdaligner.c
 create mode 100644 DALIGNER/HPCmapper.c
 create mode 100644 DALIGNER/LA4Falcon.c
 create mode 100644 DALIGNER/LA4Ice.c
 create mode 100644 DALIGNER/LAcat.c
 create mode 100644 DALIGNER/LAcheck.c
 create mode 100644 DALIGNER/LAdump.c
 create mode 100644 DALIGNER/LAindex.c
 create mode 100644 DALIGNER/LAmerge.c
 create mode 100644 DALIGNER/LAshow.c
 create mode 100644 DALIGNER/LAsort.c
 create mode 100644 DALIGNER/LAsplit.c
 create mode 100644 DALIGNER/LICENSE
 create mode 100644 DALIGNER/Makefile
 create mode 100644 DALIGNER/README
 create mode 100644 DALIGNER/README_PB.md
 create mode 100644 DALIGNER/align.c
 create mode 100644 DALIGNER/align.h
 create mode 100644 DALIGNER/daligner.c
 create mode 100644 DALIGNER/daligner_p.c
 create mode 100644 DALIGNER/filter.c
 create mode 100644 DALIGNER/filter.h
 create mode 100644 DALIGNER/filter_p.c
 create mode 100644 DALIGNER/py_utils/DAPI.py
 create mode 100644 DALIGNER/py_utils/DAPipe.py
 create mode 100644 DALIGNER/py_utils/DBLA_to_falcon.py
 create mode 100644 DALIGNER/py_utils/FALCON_ASM_NOTE
 create mode 100644 DALIGNER/py_utils/LAPI.py
 create mode 100644 DALIGNER/py_utils/LAPipe.py
 create mode 100644 DAZZ_DB/Catrack.c
 create mode 100644 DAZZ_DB/DAM2fasta.c
 create mode 100644 DAZZ_DB/DB.c
 create mode 100644 DAZZ_DB/DB.h
 create mode 100644 DAZZ_DB/DB2fasta.c
 create mode 100644 DAZZ_DB/DB2quiva.c
 create mode 100644 DAZZ_DB/DBdump.c
 create mode 100644 DAZZ_DB/DBdust.c
 create mode 100644 DAZZ_DB/DBrm.c
 create mode 100644 DAZZ_DB/DBshow.c
 create mode 100644 DAZZ_DB/DBsplit.c
 create mode 100644 DAZZ_DB/DBstats.c
 create mode 100644 DAZZ_DB/DBupgrade.Dec.31.2014.c
 create mode 100644 DAZZ_DB/DBupgrade.Sep.25.2014.c
 create mode 100644 DAZZ_DB/DUSTupgrade.Jan.1.2015.c
 create mode 100644 DAZZ_DB/GNUmakefile
 create mode 100644 DAZZ_DB/LICENSE
 create mode 100644 DAZZ_DB/Makefile
 create mode 100644 DAZZ_DB/QV.c
 create mode 100644 DAZZ_DB/QV.h
 create mode 100644 DAZZ_DB/README
 create mode 100644 DAZZ_DB/fasta2DAM.c
 create mode 100644 DAZZ_DB/fasta2DB.c
 create mode 100644 DAZZ_DB/quiva2DB.c
 create mode 100644 DAZZ_DB/simulator.c
 delete mode 100644 test/cpp/.gitignore

-- 
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